8SW8 | pdb_00008sw8

Crystal Structure of HaloTag7 bound to JF669-HaloTag ligand

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6U32

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	295	0.2 M ammonium phosphate monobasic, 0.1 M TRIS pH 8.5, 50% v/v (+/-)-2-methyl-2,4-pentanediol

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.741	α = 90
b = 62.741	β = 90
c = 163.548	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315r		2020-12-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	1.0006	ALS	8.2.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.9	58.647	99.6	0.988	23	26.3		26532

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.94	98.9		0.904

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.9	58.647	26365	1325	98.886	0.196	0.1935	0.21	0.2461	0.26	22.595

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
1.198			1.198		-2.396

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.637
r_dihedral_angle_4_deg	23.117
r_dihedral_angle_3_deg	14.772
r_dihedral_angle_1_deg	6.361
r_lrange_it	4.778
r_lrange_other	4.73
r_scangle_it	3.831
r_scangle_other	3.83
r_scbond_it	2.517
r_scbond_other	2.516
r_mcangle_it	2.45
r_mcangle_other	2.449
r_mcbond_it	1.733
r_mcbond_other	1.733
r_angle_refined_deg	1.662
r_angle_other_deg	1.353
r_nbd_other	0.243
r_symmetry_xyhbond_nbd_refined	0.217
r_nbd_refined	0.203
r_symmetry_nbd_other	0.178
r_nbtor_refined	0.176
r_xyhbond_nbd_refined	0.172
r_symmetry_nbd_refined	0.171
r_chiral_restr	0.088
r_symmetry_nbtor_other	0.079
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2351
Nucleic Acid Atoms
Solvent Atoms	173
Heterogen Atoms	52

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing